DFT performance for the hole transfer parameters in DNA π stacks

Abstract

Recently, we showed that unoccupied Kohn-Sham (KS) orbitals stemming from DFT calculations of a neutral system can be used to derive accurate estimates of the free energy and electronic couplings for excess electron transfer in DNA (Félix and Voityuk, J Phys Chem A 2008, 112, 9043). In this article, we consider the propagation of radical cation states (hole transfer) through DNA p-stacks and compare the performance of different exchange-correlation functionals to estimate the hole transfer (HT) parameters. Two different approaches are used: (1) calculations that use occupied KS orbitals of neutral p stacks of nucleobases, and (2) the time-dependent DFT method which is applied to the radical cation states of these stacks. Comparison of the calculated parameters with the reference data suggests that the best results are provided by the KS scheme with hybrid functionals (B3LYP, PBE0, and BH&HLYP). The TD DFT approach gives significantly less accurate values of the HT parameters. In agreement with high-level ab initio results, the KS scheme predicts that the hole in p stacks is confined to a single nucleobase; in contrast, the spin-unrestricted DFT method considerably overestimates the hole delocalization in the radical cations.

In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase – Cytochrome c

“…It means that excess charge delocalization in radical cations and radical anions computed by DFT may be considerably overestimated. It was shown, however, for different functionals that the excess charge distribution is well described by Kohn-Sham orbitals of neutral dimers [69]. An alternative promising approach is the construction of the diabatic Hamiltonian using charge-localized broken-symmetry states [70].…”

Ecoupling server: A tool to compute and analyze electronic couplings

“…The orbital analysis ( Figure 2) shows HOMO mainly placed on the donor (red bar) with a small proportion of acceptor (blue bar) whereas the opposite situation is found for HOMO-1. Table 1 shows the energy difference between the HOMO (assigned to donor) and HOMO-1 (acceptor), EC values computed with the ecoupling server and the published EC 25,40,41 . EC values computed with the ecupling server are in agreement with the published results showing no representative differences (<10 -3 eV).…”

Electron transfer in DNA

“…Accurate QM results obtained for simple systems provide also useful reference data to test the performance of approximate schemes. For instance, the results of MS‐CASPT2 calculations of ET parameters in stacked nucleobases43,44 have been used to estimate the performance of density functional theory (DFT)36,45–47 and semiempirical methods 48…”